Robbie Cattanach scored either side of halftime before substitute Jamie Garside added a third with just over 20 minutes remaining.
Hills were competitive against their more illustrious Telechoice Premier League opponents, who were close to full strength.
Last year?s Tiger Turf runners up were slow to get out of the blocks after their loss to Bankstown City Lions on Sunday but did enough to progress to the final eight.
Manly were best served by Cameron Jones who produced an industrious display in the middle of the park along with left back Shaun Bowden, on the comeback trail after a serious knee injury.
Manly United 3 (Robbie Cattanach 28? 53? Jamie Garside 67?) defeated Hills United 0
-By Andrew Hurrell